Methods that allow highly specific detection of nucleic acids sequences, i.e., that permit discrimination between closely related sequences, including similar or related sequences differing by only a single base, are important in various applications, including, for example, detecting or distinguishing between multimember gene families, microRNAs (miRNAs), viral serotypes, or genetic variation between individuals. Highly specific detection methods are generally complex and require numerous steps, and therefore, are not suitable for use in a high throughput format. Methods that are amenable to high throughput, such as nucleic acid microarrays, typically rely solely on nucleic acid hybridization for specificity and therefore have a limited ability to distinguish between closely related sequences.
There is a need in the art for a method of detecting or discriminating between nucleic acid sequences having high specificity and that is amenable to a high throughput format, such as microarrays. The method would be generally useful in a variety of applications requiring